Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics

Wnt signaling and polarity in freshwater sponges

(2018) Pamela J. Windsor Reid et al.   BMC EVOLUTIONARY BIOLOGY

New genomic data and analyses challenge the traditional vision of animal epithelium evolution

(2018) Hassiba Belahbib et al.   BMC GENOMICS

Evidence of Signaling and Adhesion Roles for β-Catenin in the Sponge Ephydatia muelleri

(2018) Klaske J Schippers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

(2017) Warren R. Francis et al.   Genome Biology and Evolution

Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)

(2017) Christian R. Voolstra et al.   INVERTEBRATE SYSTEMATICS

Expression of eukaryotic-like protein in the microbiome of sponges

(2017) C. Díez-Vives et al.   MOLECULAR ECOLOGY

Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA

(2017) Alexander V. Ereskovsky et al.   PLoS One

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

(2017) Heidi G. Parker et al.   Cell Reports

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

(2017) Zhiqiang Ye et al.   G3-Genes Genomes Genetics

Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues

(2017) Aaron L Fidler et al.   eLife

Ctenophore relationships and their placement as the sister group to all other animals

(2017) Nathan V. Whelan et al.   Nature Ecology & Evolution

Dating early animal evolution using phylogenomic data

(2017) Martin Dohrmann et al.   Scientific Reports

Animal multicellularity and polarity without Wnt signaling

(2017) Quentin Schenkelaars et al.   Scientific Reports

Retracing the path of planar cell polarity

(2016) Quentin Schenkelaars et al.   BMC EVOLUTIONARY BIOLOGY

Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini

(2016) Ilya Borisenko et al.   BMC EVOLUTIONARY BIOLOGY

Hologenome analysis of two marine sponges with different microbiomes

(2016) Taewoo Ryu et al.   BMC GENOMICS

A sisterly dispute

(2016) Maximilian J. Telford et al.   NATURE

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets

(2016) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Miscues misplace sponges

(2016) Kenneth M. Halanych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

An ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge

(2016) Nobuo Ueda et al.   Scientific Reports

Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome

(2016) Selene L. Fernandez-Valverde et al.   Scientific Reports

Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum

(2016) Sofia A. V. Fortunato et al.   EvoDevo

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

(2015) Marek L. Borowiec et al.   BMC GENOMICS

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

(2015) Selene L Fernandez-Valverde et al.   BMC GENOMICS

Insights into Frizzled evolution and new perspectives

(2015) Quentin Schenkelaars et al.   EVOLUTION & DEVELOPMENT

Proposal for a revised classification of the Demospongiae (Porifera)

(2015) Christine Morrow et al.   Frontiers in Zoology

The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa

(2015) Andreas Schüler et al.   Genome Biology and Evolution

Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians

(2015) N. V. Whelan et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Elements of a 'nervous system' in sponges

(2015) S. P. Leys   JOURNAL OF EXPERIMENTAL BIOLOGY

The ctenophore lineage is older than sponges? That cannot be right! Or can it?

(2015) K. M. Halanych   JOURNAL OF EXPERIMENTAL BIOLOGY

Nothing in (sponge) biology makes sense – except when based on holotypes

(2015) Dirk Erpenbeck et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals

(2015) Sofia A.V. Fortunato et al.   Marine Genomics

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

(2015) E. Sally Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The hidden biology of sponges and ctenophores

(2015) Casey W. Dunn et al.   TRENDS IN ECOLOGY & EVOLUTION

Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona(Soestella)caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific

(2015) Ingrid S. Knapp et al.   PeerJ

Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges

(2014) Danielle A Ludeman et al.   BMC EVOLUTIONARY BIOLOGY

The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals

(2014) Arunkumar Krishnan et al.   BMC EVOLUTIONARY BIOLOGY

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

(2014) Ana Riesgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans

(2014) Sven Leininger et al.   Nature Communications

History of a prolific family: the Hes/Hey-related genes of the annelid Platynereis

(2014) Eve Gazave et al.   EvoDevo

A first exploration of genome size diversity in sponges

(2013) Nicholas W. Jeffery et al.   GENOME

Novel Scenarios of Early Animal Evolution--Is It Time to Rewrite Textbooks?

(2013) M. Dohrmann et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The Integrative Taxonomic Approach Applied to Porifera: A Case Study of the Homoscleromorpha

(2013) N. Boury-Esnault et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species

(2013) Eve Gazave et al.   PLoS One

Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity

(2013) Jeffrey H. Ringrose et al.   Nature Communications

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Cellular and molecular processes leading to embryo formation in sponges: evidences for high conservation of processes throughout animal evolution

(2012) Alexander V. Ereskovsky et al.   DEVELOPMENT GENES AND EVOLUTION

A unique alkaline pH-regulated and fatty acid-activated tandem pore domain potassium channel (K2P) from a marine sponge

(2012) G. D. Wells et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin

(2012) A. S. Rivera et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

(2012) Oliver Voigt et al.   PLoS One

Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/ -catenin complex

(2012) S. A. Nichols et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functionalization of a protosynaptic gene expression network

(2012) C. Conaco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metazoan opsin evolution reveals a simple route to animal vision

(2012) R. Feuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns

(2012) Sofia Fortunato et al.   EvoDevo

RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria

(2011) Ajna S Rivera et al.   BMC BIOTECHNOLOGY

No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera

(2011) Eve Gazave et al.   HYDROBIOLOGIA

Epithelia, an Evolutionary Novelty of Metazoans

(2011) Sally P. Leys et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The Evolutionary History of YAP and the Hippo/YAP Pathway

(2011) D. Hilman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

(2010) Alexandre Alié et al.   BMC EVOLUTIONARY BIOLOGY

A conserved germline multipotency program

(2010) C. E. Juliano et al.   DEVELOPMENT

Structure of the central nervous system of a juvenile acoel, Symsagittifera roscoffensis

(2010) Amandine Bery et al.   DEVELOPMENT GENES AND EVOLUTION

Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica

(2010) Maja Adamska et al.   EVOLUTION & DEVELOPMENT

Wnt signaling and induction in the sponge aquiferous system: evidence for an ancient origin of the organizer

(2010) Pamela J. Windsor et al.   EVOLUTION & DEVELOPMENT

Origin of animal epithelia: insights from the sponge genome

(2010) Bryony Fahey et al.   EVOLUTION & DEVELOPMENT

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Freshwater Sponges Have Functional, Sealing Epithelia with High Transepithelial Resistance and Negative Transepithelial Potential

(2010) Emily D. M. Adams et al.   PLoS One

Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi

(2010) Kevin Pang et al.   EvoDevo

The Homoscleromorph spongeOscarellalobularis, a promising sponge model in evolutionary and developmental biology

(2009) Alexander V. Ereskovsky et al.   BIOESSAYS

Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes

(2009) Eve Gazave et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Origin of the neuro-sensory system: new and expected insights from sponges

(2009) EMMANUELLE RENARD et al.   Integrative Zoology

Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa

(2009) E. A. Sperling et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early origin of the bilaterian developmental toolkit

(2009) D. H. Erwin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit

(2008) Gemma S. Richards et al.   CURRENT BIOLOGY

NK homeobox genes with choanocyte-specific expression in homoscleromorph sponges

(2008) Eve Gazave et al.   DEVELOPMENT GENES AND EVOLUTION

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida)

(2008) Martin Dohrmann et al.   SYSTEMATIC BIOLOGY

Sponge Cytogenetics — Mitotic Chromosomes of Ten Species of Freshwater Sponge

(2008) Junko Ishijima et al.   ZOOLOGICAL SCIENCE